2023-11-01 REL RCSB RCSB RCSB 2023-06-24 2023-11-01 2023-11-01 2023-11-01 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM45377 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM112108 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH GM117212 United States Composite multiscale structure of the yeast NPC Akey CW Echeverria I Ouch C Fernandez-Martinez J Rout MP nuclear pore complex, nucleocytoplasmic transport, nucleoporin, membrane protein, TRANSPORT PROTEIN Akey CW Echeverria I Ouch C Nudelman I Shi Y Wang J Chait BT Sali A Fernandez-Martinez J Rout MP Implications of a multiscale structure of the yeast nuclear pore complex. Mol.Cell US 83 3283 3302.e5 2023 37738963 doi:10.1016/j.molcel.2023.08.025 1097-2765 2168 MOCEFL EMD-41122 other EM volume
Connectors in cytoplasmic outer ring of yeast NPC
 EMD-41114 other EM volume
Full nuclear double outer ring of the yeast NPC
 EMD-41116 other EM volume
Lumenal ring of the isolated yeast NPC
 EMD-41119 other EM volume
Cytoplasmic outer ring of the yeast NPC
 EMD-41120 other EM volume
Central transporter/plug yeast NPC
 EMD-41121 other EM volume
Double outer ring connectors of yeast NPC
 EMD-41285 other EM volume
Double nuclear outer ring of Nup84-complexes from the yeast NPC
 EMD-41117 other EM volume
Pom34-Pom152 membrane attachment site yeast NPC
 EMD-41300 other EM volume
Inner spoke ring of the yeast NPC
 Nuclear Pore Complex Nuclear Pore Complex 0
Protein A tagged Mlp1 pullout of NPC
Saccharomyces cerevisiae MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5 nucleus nuclear envelope singleParticle particle 0.1 7.5
20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT
 Quantifoil R2/2 COPPER 400 CARBON HOLEY ARRAY 5.0 GLOW DISCHARGE OTHER ETHANE 100 283 FEI VITROBOT MARK III
One step affinity purified
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 3.5 37651.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 2-40 1 4015 40.0
3218 images retained after triage
 1 26049
C8 symmetrized inner ring map
 C8 FOURIER SPACE 28.0 FSC 0.143 CUT-OFF RELION 3.0.7 5000 MAXIMUM LIKELIHOOD RELION 3.0.7
C8 symmetry used
 MAXIMUM LIKELIHOOD RELION 3.0.7 RELION 3.0.7 emd_41123.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.06481644 0.10330972 0.003336525 0.008165721 2.66 2.66 2.66 0.0086 AUTHOR One possible Master map Other experimental model
none
 RIGID BODY FIT
Rigid body docking of 3D maps with Chimera
cross correlation REAL emd_41123_msk_1.map emd_41123_additional_18.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.0000010430952 0.037561823 0.00041275294 0.0031491572 2.66 2.66 2.66 AUTHOR segmented central transporter-plug, effectively a cylindrical average emd_41123_additional_17.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.00003162093 0.18181434 0.00007650066 0.0022744958 2.66 2.66 2.66 AUTHOR L1 linker domains - c8 ring emd_41123_additional_16.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.00012900274 0.05700091 0.000015873886 0.00057656877 2.66 2.66 2.66 AUTHOR L2 linker domains - c8 ring emd_41123_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.260719 8.174860000000001 0.0029128592 0.095573425 2.66 2.66 2.66 AUTHOR segmented densities for two putative Nic96 CTDs - c8 ring emd_41123_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.00000003616898 0.23028432 0.00033259136 0.0056869593 2.66 2.66 2.66 AUTHOR molmap model for outer copy of putative Nup188-192 c8 ring emd_41123_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.000000031647858 0.20812494 0.00033260672 0.0056557343 2.66 2.66 2.66 AUTHOR molmap model for inner copy of putative Nup188-192 c8 ring emd_41123_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -1.4365408 6.037515 0.0032293757 0.061878417 2.66 2.66 2.66 AUTHOR segmented proximal Y-complex nuclear outer ring emd_41123_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -1.568928 5.5280857 0.0027358378 0.053535398 2.66 2.66 2.66 AUTHOR segmented distal Y-complex nuclear outer ring emd_41123_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.11611575 0.3653888 -0.003482897 0.01244301 2.66 2.66 2.66 AUTHOR cytoplasmic outer ring c8 ring emd_41123_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.66977376 1.8079556 0.005565968 0.06463531 2.66 2.66 2.66 AUTHOR lumenal c8 ring emd_41123_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.66209334 0.7522464 0.0037181291 0.037158478 2.66 2.66 2.66 AUTHOR segmented micelle map-c8 ring emd_41123_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.36346307 0.70760053 0.001259996 0.0193859 2.66 2.66 2.66 AUTHOR segmented Ndc1 TMD map-c8 ring emd_41123_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.6009241 1.6932685 0.0015935651 0.034889795 2.66 2.66 2.66 AUTHOR segmented Pom34-152 TMD map-c8 ring emd_41123_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.18627715 1.6577239 0.00025416553 0.0131690465 2.66 2.66 2.66 AUTHOR segmented new connectors map-c8 ring emd_41123_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.39428797 1.6201448 0.00034856846 0.015067579 2.66 2.66 2.66 AUTHOR segmented Nic96 NTD connectors map-c8 ring emd_41123_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -1.1692456 3.9104614 0.003504579 0.060864963 2.66 2.66 2.66 AUTHOR adaptin-like c8 ring emd_41123_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.9393937 3.4701605 0.0049937526 0.06737636 2.66 2.66 2.66 AUTHOR Membrane interacting c8 ring emd_41123_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.3226017 2.4413183 0.0014112102 0.035169322 2.66 2.66 2.66 AUTHOR Nsp1 inner c8 ring emd_41123_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.032448158 0.049655348 0.0016813762 0.004394813 2.66 2.66 2.66 AUTHOR emd_41123_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.03170597 0.049788877 0.0017324312 0.004412694 2.66 2.66 2.66 AUTHOR